Sequential programmable self-assembly: Role of cooperative interactions
Abstract
We propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenient platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles.more »
- Authors:
-
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Publication Date:
- Research Org.:
- Brookhaven National Laboratory (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1255731
- Alternate Identifier(s):
- OSTI ID: 1421159
- Report Number(s):
- BNL-112267-2016-JA
Journal ID: ISSN 0021-9606; KC0403020
- Grant/Contract Number:
- SC00112704; SC0012704
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Journal of Chemical Physics
- Additional Journal Information:
- Journal Volume: 144; Journal Issue: 9; Journal ID: ISSN 0021-9606
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 77 NANOSCIENCE AND NANOTECHNOLOGY; self assembly; DNA; free energy; bond formation; colloidal systems
Citation Formats
Jonathan D. Halverson, and Tkachenko, Alexei V. Sequential programmable self-assembly: Role of cooperative interactions. United States: N. p., 2016.
Web. doi:10.1063/1.4942615.
Jonathan D. Halverson, & Tkachenko, Alexei V. Sequential programmable self-assembly: Role of cooperative interactions. United States. https://doi.org/10.1063/1.4942615
Jonathan D. Halverson, and Tkachenko, Alexei V. 2016.
"Sequential programmable self-assembly: Role of cooperative interactions". United States. https://doi.org/10.1063/1.4942615. https://www.osti.gov/servlets/purl/1255731.
@article{osti_1255731,
title = {Sequential programmable self-assembly: Role of cooperative interactions},
author = {Jonathan D. Halverson and Tkachenko, Alexei V.},
abstractNote = {We propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenient platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.},
doi = {10.1063/1.4942615},
url = {https://www.osti.gov/biblio/1255731},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 9,
volume = 144,
place = {United States},
year = {Fri Mar 04 00:00:00 EST 2016},
month = {Fri Mar 04 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
A DNA-based method for rationally assembling nanoparticles into macroscopic materials
journal, August 1996
- Mirkin, Chad A.; Letsinger, Robert L.; Mucic, Robert C.
- Nature, Vol. 382, Issue 6592, p. 607-609
Organization of 'nanocrystal molecules' using DNA
journal, August 1996
- Alivisatos, A. Paul; Johnsson, Kai P.; Peng, Xiaogang
- Nature, Vol. 382, Issue 6592
DNA-programmable nanoparticle crystallization
journal, January 2008
- Park, Sung Yong; Lytton-Jean, Abigail K. R.; Lee, Byeongdu
- Nature, Vol. 451, Issue 7178, p. 553-556
Colloidal Interactions and Self-Assembly Using DNA Hybridization
journal, February 2005
- Biancaniello, Paul L.; Kim, Anthony J.; Crocker, John C.
- Physical Review Letters, Vol. 94, Issue 5
DNA-guided crystallization of colloidal nanoparticles
journal, January 2008
- Nykypanchuk, Dmytro; Maye, Mathew M.; van der Lelie, Daniel
- Nature, Vol. 451, Issue 7178, p. 549-552
Re-entrant melting as a design principle for DNA-coated colloids
journal, April 2012
- Angioletti-Uberti, Stefano; Mognetti, Bortolo M.; Frenkel, Daan
- Nature Materials, Vol. 11, Issue 6
Nanoparticle Superlattice Engineering with DNA
journal, October 2011
- Macfarlane, R. J.; Lee, B.; Jones, M. R.
- Science, Vol. 334, Issue 6053, p. 204-208
How to build nanoblocks using DNA scaffolds
journal, October 2008
- Licata, N. A.; Tkachenko, A. V.
- EPL (Europhysics Letters), Vol. 84, Issue 2
The Free-Energy Landscape of Clusters of Attractive Hard Spheres
journal, January 2010
- Meng, G.; Arkus, N.; Brenner, M. P.
- Science, Vol. 327, Issue 5965
Design principles for self-assembly with short-range interactions
journal, March 2011
- Hormoz, S.; Brenner, M. P.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 13
Undesired usage and the robust self-assembly of heterogeneous structures
journal, February 2015
- Murugan, Arvind; Zou, James; Brenner, Michael P.
- Nature Communications, Vol. 6, Issue 1
Rational design of self-assembly pathways for complex multicomponent structures
journal, May 2015
- Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 20
DNA-programmed mesoscopic architecture
journal, June 2013
- Halverson, Jonathan D.; Tkachenko, Alexei V.
- Physical Review E, Vol. 87, Issue 6
Switchable self-protected attractions in DNA-functionalized colloids
journal, June 2009
- Leunissen, Mirjam E.; Dreyfus, Rémi; Cheong, Fook Chiong
- Nature Materials, Vol. 8, Issue 7
Folding DNA to create nanoscale shapes and patterns
journal, March 2006
- Rothemund, Paul W. K.
- Nature, Vol. 440, Issue 7082, p. 297-302
Specific Binding of Different Vesicle Populations by the Hybridization of Membrane-Anchored DNA †
journal, December 2007
- Beales, Paul A.; Vanderlick, T. Kyle
- The Journal of Physical Chemistry A, Vol. 111, Issue 49
Mobile Linkers on DNA-Coated Colloids: Valency without Patches
journal, September 2014
- Angioletti-Uberti, Stefano; Varilly, Patrick; Mognetti, Bortolo M.
- Physical Review Letters, Vol. 113, Issue 12
Solid Colloids with Surface-Mobile DNA Linkers
journal, September 2013
- van der Meulen, Stef A. J.; Leunissen, Mirjam E.
- Journal of the American Chemical Society, Vol. 135, Issue 40
Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes
journal, January 2015
- Parolini, Lucia; Mognetti, Bortolo M.; Kotar, Jurij
- Nature Communications, Vol. 6, Issue 1
Works referencing / citing this record:
Multivalent “attacker and guard” strategy for targeting surfaces with low receptor density
journal, May 2019
- Tito, Nicholas B.
- The Journal of Chemical Physics, Vol. 150, Issue 18
Spontaneous emergence of catalytic cycles with colloidal spheres
journal, April 2017
- Zeravcic, Zorana; Brenner, Michael P.
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 17
Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces
journal, October 2019
- Mognetti, Bortolo Matteo; Cicuta, Pietro; Di Michele, Lorenzo
- Reports on Progress in Physics, Vol. 82, Issue 11
Multivalent "Attacker & Guard" Strategy for Targeting Surfaces with Low Receptor Density
text, January 2018
- Tito, Nicholas B.
- arXiv
Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces
text, January 2019
- Mognetti, Bortolo; Cicuta, Pietro; Di Michele, Lorenzo
- arXiv
Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces
text, January 2019
- Mognetti, Bortolo; Cicuta, Pietro; Di Michele, Lorenzo
- arXiv